A lot of people seem to recommend 5 officers. I have found it easier to use 4 officers. That way I can have 2 officers working and 2 resting most of the time.

I usually divide all my crew into 2 shifts, except for torpedo crew, and then switch everyone around at the same time when needed. Each shift consists of:

2 engine POs
3 engine crew
3 control room crew
1 radio PO
1 radio crew
1 watch PO
3 watch crew

So, I have 2 sets of those, one resting and one at work. When submerged, both watch crews are resting. To have enough room to rest the second watch crew when submerged, this leaves me with 6 more PO/crew slots for other crew on a type VII. On a type IX, I think I'd have room for 4 more. I currently have:

4 torpedo PO
1 repair PO
1 medic PO

I'm probably going to get rid of the medic and take a flak PO instead. This crew is used to load torpedoes. In case I need crew loading both bow and stern torpedoes, I have torpedo qualification on 2 officers, and might occasionally use resting watch (when submerged) or control room (when on surface) crew to help load torpedoes.

As for officers, I have 2 officers with control room qualification, and they take turns at the left most slot in the control room. The navigation and weapons officer slots are empty when cruising, and filled only when needed. The other 2 officers both have watch qualification, and they take turns on the bridge.

When I submerge, the watch officer currently on duty goes to either the navigation or the weapons position, depending on if I'm planning to attack something or not. So normally, during submerged attacks, I can still have 2 officers resting.

As for officer qualifications, I currently use the following combination, and have found it works well:

The officers alternating on control room duty:
repair, helm, engine
helm, torpedo, medic

I never have any real use for the engine qualification, but it just feels logical to me to have.

The watch officers have:
watch, deck gun, flak
watch, torpedo, flak or watch, torpedo, repair

Haven't decided yet which is more useful for the second watch officer, flak or repair.

I also tried the "no fatigue" and found it hurt the immersive quality. I've stuck with the 8-hour model from then on.

You don't have to sail around at 1x to have your men recover. They'll recover at 32x just fine...but higher than that the fatigue model turns off. Sail around a little at 32x and they recover pretty fast.

Im now using No fatigue in my latest career, and im enjoying the game much more.
No more going onto the crew screen every few minutes to check how worn out my crew are.

The crew management feature is totally lacking. I want to be able to manage supplies--food--and the cleaning of the washrooms.:p

I'm fatigued just reading all this.

No fatigue for me.